Human DNA sequences: more variation and less race

The need to incorporate human variation and evolutionary theory in forensic anthropology: A call for reform

In 1992, Norm Sauer called for a language shift in which practitioners would move away from the socially loaded term "race" and replace it with the less provocative term "ancestry." While many heeded the call and moved towards ancestry in their research and reports, the actual approach to research and analysis did not change. In response to this change, there was a large growth in ancestry estimation method development in the early decade of the 2000s. However, the practice of ancestry estimation did not adequately incorporate evolutionary theory in interpretation or trait selection and continued with little critical reflection. In the past decade, there has been an increase in ancestry validation methods with little critique of the "race" concept or discussion of modern human variation or reference samples. To advance, forensic anthropologists need to reckon with the practice of ancestry estimation as it is currently practiced. We are calling for another reform in the axiom focusing on evolutionary theory, population history, trait selection, and population-level reference samples. The practice needs to abandon the terms ancestry and race completely and recalibrate to an analysis of population affinity. Population affinity is a statistical approach based on the underlying population structure that would allow the understanding of how microevolutionary forces act in concert with historical events (e.g., colonization, the Transatlantic Slave Trade, etc.) to shape modern human variation. This is not to be confused with geographic ancestry that all too often can be perceived as interchangeable with social race and as an affirmation of the biological concept of race. It is time to critically evaluate the social and scientific implications of the current practice of ancestry estimation, and re-frame our approach to studying and analyzing modern human variation through a population structure approach.

Shaping birth: variation in the birth canal and the importance of inclusive obstetric care

Regional variation in pelvic morphology and childbirth has long occurred alongside traditional labour support and an understanding of possible normal courses of childbirth for each population. The process of migration and globalization has broken down these links, while a European model of 'normal' labour has become widespread. The description of 'normal' childbirth provided within obstetrics and midwifery textbooks, in fact, is modelled on a specific pelvic morphology that is common in European women. There is mounting evidence, however, that this model is not representative of women's diversity, especially for women of non-white ethnicities. The human birth canal is very variable in shape, both within and among human populations, and differences in pelvic shapes have been associated with differences in the mechanism of labour. Normalizing a white-centred model of female anatomy and of childbirth can disadvantage women of non-European ancestry. Because they are less likely to fit within this model, pelvic shape and labour pattern in non-white women are more likely to be considered 'abnormal', potentially leading to increased rates of labour intervention. To ensure that maternal care is inclusive and as safe as possible for all women, obstetric and midwifery training need to incorporate women's diversity. This article is part of the theme issue 'Multidisciplinary perspectives on social support and maternal-child health'.

How strong was the bottleneck associated to the peopling of the Americas? New insights from multilocus sequence data

In spite of many genetic studies that contributed for a deep knowledge about the peopling of the Americas, no consensus has emerged about important parameters such as the effective size of the Native Americans founder population. Previous estimates based on genomic datasets may have been biased by the use of admixed individuals from Latino populations, while other recent studies using samples from Native American individuals relied on approximated analytical approaches. In this study we use resequencing data for nine independent regions in a set of Native American and Siberian individuals and a full-likelihood approach based on isolation-with-migration scenarios accounting for recent flow between Asian and Native American populations. Our results suggest that, in agreement with previous studies, the effective size of the Native American population was small, most likely in the order of a few hundred individuals, with point estimates close to 250 individuals, even though credible intervals include a number as large as ~4,000 individuals. Recognizing the size of the genetic bottleneck during the peopling of the Americas is important for determining the extent of genetic markers needed to characterize Native American populations in genome-wide studies and to evaluate the adaptive potential of genetic variants in this population.

Implementation of genomics research in Africa: challenges and recommendations

BACKGROUND

There is exponential growth in the interest and implementation of genomics research in Africa. This growth has been facilitated by the Human Hereditary and Health in Africa (H3Africa) initiative, which aims to promote a contemporary research approach to the study of genomics and environmental determinants of common diseases in African populations.

OBJECTIVE

The purpose of this article is to describe important challenges affecting genomics research implementation in Africa.

METHODS

The observations, challenges and recommendations presented in this article were obtained through discussions by African scientists at teleconferences and face-to-face meetings, seminars at consortium conferences and in-depth individual discussions.

RESULTS

Challenges affecting genomics research implementation in Africa, which are related to limited resources include ill-equipped facilities, poor accessibility to research centers, lack of expertise and an enabling environment for research activities in local hospitals. Challenges related to the research study include delayed funding, extensive procedures and interventions requiring multiple visits, delays setting up research teams and insufficient staff training, language barriers and an underappreciation of cultural norms. While many African countries are struggling to initiate genomics projects, others have set up genomics research facilities that meet international standards.

CONCLUSIONS

The lessons learned in implementing successful genomics projects in Africa are recommended as strategies to overcome these challenges. These recommendations may guide the development and application of new research programs in low-resource settings.

A Qualitative Analysis of How Anthropologists Interpret the Race Construct

This article assesses anthropological thinking about the race concept and its applications. Drawn from a broader national survey of geneticists' and anthropologists' views on race, in this analysis, we provide a qualitative account of anthropologists' perspectives. We delve deeper than simply asserting that "race is a social construct." Instead, we explore the differential ways in which anthropologists describe and interpret how race is constructed. Utilizing the heuristic of constructors, shifters, and reconcilers, we also illustrate the ways in which anthropologists conceptualize their interpretations of race along a broad spectrum as well as what these differential approaches reveal about the ideological and biological consequences of socially defined races, such as racism in general and racialized health disparities in particular. [race concept, social construction, racism, health disparities].

Population Genomics and the Statistical Values of Race: An Interdisciplinary Perspective on the Biological Classification of Human Populations and Implications for Clinical Genetic Epidemiological Research

The biological status and biomedical significance of the concept of race as applied to humans continue to be contentious issues despite the use of advanced statistical and clustering methods to determine continental ancestry. It is thus imperative for researchers to understand the limitations as well as potential uses of the concept of race in biology and biomedicine. This paper deals with the theoretical assumptions behind cluster analysis in human population genomics. Adopting an interdisciplinary approach, it demonstrates that the hypothesis that attributes the clustering of human populations to "frictional" effects of landform barriers at continental boundaries is empirically incoherent. It then contrasts the scientific status of the "cluster" and "cline" constructs in human population genomics, and shows how cluster may be instrumentally produced. It also shows how statistical values of race vindicate Darwin's argument that race is evolutionarily meaningless. Finally, the paper explains why, due to spatiotemporal parameters, evolutionary forces, and socio-cultural factors influencing population structure, continental ancestry may be pragmatically relevant to global and public health genomics. Overall, this work demonstrates that, from a biological systematic and evolutionary taxonomical perspective, human races/continental groups or clusters have no natural meaning or objective biological reality. In fact, the utility of racial categorizations in research and in clinics can be explained by spatiotemporal parameters, socio-cultural factors, and evolutionary forces affecting disease causation and treatment response.

Common Variants and Haplotypes in the TF, TNF-α, and TMPRSS6 Genes Are Associated with Iron Status in a Female Black South African Population

BACKGROUND

It is unknown whether single nucleotide polymorphisms (SNPs), associated with iron status in European and Asian populations, have the same relation within the African population.

OBJECTIVES

We investigated associations of reported SNPs with iron markers in a South African cohort.

METHODS

Hemoglobin concentration, serum ferritin (SF) and soluble transferrin receptor (sTfR) concentrations, and body iron (BI) stores were measured in women (n = 686; range, 32-86 y) who were part of the Prospective Urban and Rural Epidemiology study. Thirty-two SNPs in 12 genes were selected based on existing genome-wide association study data.

RESULTS

In the transferrin (TF) gene, SF and BI were significantly lower in the heterozygote genotype (AG) of reference SNP (rs) 1799852 (P = 0.01 and 0.03, respectively) and sTfR concentrations were significantly higher (P = 0.004) than the homozygote minor allele genotype (AA), whereas transferrin receptor and BI concentrations were significantly lower in the heterozygote genotype (AG) of rs3811647 (both P = 0.03) than the homozygote wild-type (AA) and minor allele groups (GG). The chromosome 6 allele combination (AAA) consisting of rs1799964 and rs1800629 both in tumor necrosis factor-α (TNF-α) and rs2071592 in nuclear factor κB inhibitor-like protein 1 (NFKBIL1) was associated with higher odds for low SF concentrations (SF < 15 μg/L; OR: 1.86; 95% CI: 1.23, 2.79) than the allele combinations AGA, GGT, and AGT. The chromosome 22 allele combination (GG) consisting of rs228918 and rs228921 in the transmembrane protease serine 6 (TMPRSS6) gene was associated with lower odds for increased sTfR concentrations (sTfR > 8.3mg/L; OR: 0.79; 95% CI: 0.63, 0.98) than the allele combination AA.

CONCLUSIONS

Various SNPs and allele combinations in the TF, TNF-α, and TMPRSS6 genes are associated with iron status in black South African women; however, these association patterns are different compared with European ancestry populations. This stresses the need for population-specific genomic data.

An evaluation of nasal bone and aperture shape among three South African populations

Reliable and valid population specific standards are necessary to accurately develop a biological profile, which includes an estimation of peer-reported social identification (Hefner, 2009). During the last 300 years, colonialism, slavery and apartheid created geographic, physical and social divisions of population groups in South Africa. The purpose of this study was to evaluate variation in nasal bone and aperture shape in a modern population of black, white, and coloured South Africans using standard craniometric variables and geometric morphometrics, namely general Procrustes and elliptical Fourier analyses. Fourteen standard landmarks were digitally recorded or computationally derived from 310 crania using a 3D coordinate digitizer for discriminant function, principal components and generalized Procrustes analyses. For elliptical Fourier analysis, outlines of the nasal aperture were generated from standardized photographs. All classification accuracies were better than chance; the lowest accuracies were for coloured and the highest accuracies were for white South Africans. Most difficulties arose in distinguishing coloured and black South African groups from each other. Generally, misclassifications were noted between the sexes within each group rather than among groups, which suggests that sex has less influence on nasal bone and aperture shape than ancestry. Quantifiable variation in shape of the nasal aperture region between white and non-white South African groups was observed.

Genetic population structure accounts for contemporary ecogeographic patterns in tropic and subtropic-dwelling humans

Contemporary human populations conform to ecogeographic predictions that animals will become more compact in cooler climates and less compact in warmer ones. However, it remains unclear to what extent this pattern reflects plastic responses to current environments or genetic differences among populations. Analyzing anthropometric surveys of 232,684 children and adults from across 80 ethnolinguistic groups in sub-Saharan Africa, Asia and the Americas, we confirm that body surface-to-volume correlates with contemporary temperature at magnitudes found in more latitudinally diverse samples (Adj. R² = 0.14-0.28). However, far more variation in body surface-to-volume is attributable to genetic population structure (Adj. R² = 0.50-0.74). Moreover, genetic population structure accounts for nearly all of the observed relationship between contemporary temperature and body surface-to-volume among children and adults. Indeed, after controlling for population structure, contemporary temperature accounts for no more than 4% of the variance in body form in these groups. This effect of genetic affinity on body form is also independent of other ecological variables, such as dominant mode of subsistence and household wealth per capita. These findings suggest that the observed fit of human body surface-to-volume with current climate in this sample reflects relatively large effects of existing genetic population structure of contemporary humans compared to plastic response to current environments.

Ecogeography, genetics, and the evolution of human body form

Genetic resemblances among groups are non-randomly distributed in humans. This population structure may influence the correlations between traits and environmental drivers of natural selection thus complicating the interpretation of the fossil record when modern human variation is used as a referential model. In this paper, we examine the effects of population structure and natural selection on postcranial traits that reflect body size and shape with application to the more general issue of how climate - using latitude as a proxy - has influenced hominin morphological variation. We compare models that include terms reflecting population structure, ascertained from globally distributed microsatellite data, and latitude on postcranial phenotypes derived from skeletal dimensions taken from a large global sample of modern humans. We find that models with a population structure term fit better than a model of natural selection along a latitudinal cline in all cases. A model including both latitude and population structure terms is a good fit to distal limb element lengths and bi-iliac breadth, indicating that multiple evolutionary forces shaped these morphologies. In contrast, a model that included only a population structure term best explained femoral head diameter and the crural index. The results demonstrate that population structure is an important part of human postcranial variation, and that clinally distributed natural selection is not sufficient to explain among-group differentiation. The distribution of human body form is strongly influenced by the contingencies of modern human origins, which calls for new ways to approach problems in the evolution of human variation, past and present.

BiDil in the Clinic: An Interdisciplinary Investigation of Physicians' Prescription Patterns of a Race-Based Therapy

BACKGROUND

The African American Heart Failure Trial (A-HeFT) and the FDA approval of BiDil for race-specific prescription have stirred the debate about the scientific and medical status of race. Yet there is no assessment of the potential fallouts of this dispute on physicians' willingness to prescribe the drug. We present here an analysis of the factors influencing physicians' prescription of BiDil and investigate whether exposure to the controversy has an impact on their therapeutic judgments about the drug.

METHODS

We conducted an electronic survey with physicians in the department of internal medicine at the University of Cincinnati. Participants were randomly assigned to two groups, with one group receiving information about the controversy over BiDil. We used various statistical tests, including a linear mixed effects model, to analyze the results.

RESULTS

27% of the participants reported using patients' race as a major factor in making treatment decisions. 33% reported the inefficacy of standard therapies, 25% the severity of the disease, and 15% other unspecified factors as primary determining criteria in prescribing BiDil. With respect to the controversy, 68% of physicians reported that they were not aware of any controversy surrounding BiDil. Physicians' willingness to prescribe BiDil as a therapy was associated with their awareness of the controversy surrounding A-HeFT (p < 0.003). But their willingness to prescribe the therapy along racial lines did not vary significantly with exposure to the controversy.

CONCLUSIONS

Overall, physicians prescribe and are willing to prescribe BiDil more to black patients than to white patients. However, physicians' lack of awareness about the controversial scientific status of A-HeFT suggests the need for more efficient ways to convey scientific information about BiDil to clinicians. Furthermore, the uncertainties about the determination of clinical utility of BiDil for the individual patient raise questions about whether this specific race-based therapy is in patients' best interest.

Nine things to remember about human genome diversity

Understanding how and why humans are biologically different is indispensable to get oriented in the ever-growing body of genomic data. Here we discuss the evidence based on which we can confidently state that humans are the least genetically variable primate, both when individuals and when populations are compared, and that each individual genome can be regarded as a mosaic of fragments of different origins. Each population is somewhat different from any other population, and there are geographical patterns in that variation. These patterns clearly indicate an African origin for our species, and keep a record of the main demographic changes accompanying the peopling of the whole planet. However, only a minimal fraction of alleles, and a small fraction of combinations of alleles along the chromosome, is restricted to a single geographical region (and even less so to a single population), and diversity between members of the same population is very large. The small genomic differences between populations and the extensive allele sharing across continents explain why historical attempts to identify, once and for good, major biological groups in humans have always failed. Nevertheless, racial categorization is all but gone, especially in clinical studies. We argue that racial labels may not only obscure important differences between patients but also that they have become positively useless now that cheap and reliable methods for genotyping are making it possible to pursue the development of truly personalized medicine.

Rejection of a serial founder effects model of genetic and linguistic coevolution

Recent genetic studies attribute the negative correlation between population genetic diversity and distance from Africa to a serial founder effects (SFE) evolutionary process. A recent linguistic study concluded that a similar decay in phoneme inventories in human languages was also the product of the SFE process. However, the SFE process makes additional predictions for patterns of neutral genetic diversity, both within and between groups, that have not yet been tested on phonemic data. In this study, we describe these predictions and test them on linguistic and genetic samples. The linguistic sample consists of 725 widespread languages, which together contain 908 distinct phonemes. The genetic sample consists of 614 autosomal microsatellite loci in 100 widespread populations. All aspects of the genetic pattern are consistent with the predictions of SFE. In contrast, most of the predictions of SFE are violated for the phonemic data. We show that phoneme inventories provide information about recent contacts between languages. However, because phonemes change rapidly, they cannot provide information about more ancient evolutionary processes.

The impact of founder effects, gene flow, and European admixture on native American genetic diversity

Recent studies have concluded that the global pattern of neutral genetic diversity in humans reflects a series of founder effects and population movements associated with our recent expansion out of Africa. In contrast, regional studies tend to emphasize the significance of more complex patterns of colonization, gene flow, and secondary population movements in shaping patterns of diversity. Our objective in this study is to examine how founder effects, gene flow, and European admixture have molded patterns of neutral genetic diversity in the Americas. Our strategy is to test the fit of a serial founder effects process to the pattern of neutral autosomal genetic variation and to examine the contribution of gene flow and European admixture to departures from fit. The genetic data consist of 678 autosomal microsatellite loci assayed by Wang and colleagues in 530 individuals in 29 widely distributed Native American populations. We find that previous evidence for serial founder effects in the Americas may be driven in part by high levels of European admixture in northern North America, intermediate levels in Central America, and low levels in eastern South America. Geographically patterned admixture may also account for previously reported genetic differences between Andean and Amazonian groups. Though admixture has obscured the precise details of precontact evolutionary processes, we find that genetic diversity is still largely hierarchically structured and that gene flow between neighboring groups has had surprisingly little impact on macrogeographic patterns of genetic diversity in the Americas.

Ossification of the posterior longitudinal ligament in non-Asians: demographic, clinical, and radiographic findings in 43 patients

Object

Ossification of the posterior longitudinal ligament (OPLL) is a disorder afflicting as many as 2% of East Asians. However, reports of OPLL in non-Asians have been sporadic in the medical literature. This study describes clinical and radiographic findings with OPLL in non-Asians at a tertiary care center treating a diverse multiethnic population.

Methods

Over a 6-year period, 43 patients not of East Asian descent presented to an urban tertiary medical center with OPLL. Patient data, including ethnicity, spinal cord function, Nurick grade, radiographic findings, OPLL subtype, and degree of cervical stenosis, were recorded.

Results

The average patient age was 59 years (range 32–92 years) with 18 women and 25 men. There were 22 Caucasian patients, 17 Hispanic patients, and 4 Black patients. With respect to the radiographic findings, OPLL morphology was continuous in 19, segmental in 17, mixed in 6, and other in 1. Average canal diameter was 7.6 mm (range 4.2–9.0 mm) at the most stenotic points. The mean Nurick grade was 2.95 at presentation, but 7 of the patients had OPLL identified incidentally and with early or minimal symptoms and signs of myelopathy.

Conclusions

Ossification of the posterior longitudinal ligament in non-Asians demonstrates similar demographic and radiographic characteristics as in East Asians. The representation of different ethnic groups mirrors the demographics of the medical center population in general, showing no specific predilection for particular ethnic groups. Surgical decompression in appropriately selected patients results in similar rates of improvement when compared with the Japanese literature.

The evolution of human genetic and phenotypic variation in Africa

Africa is the birthplace of modern humans, and is the source of the geographic expansion of ancestral populations into other regions of the world. Indigenous Africans are characterized by high levels of genetic diversity within and between populations. The pattern of genetic variation in these populations has been shaped by demographic events occurring over the last 200,000 years. The dramatic variation in climate, diet, and exposure to infectious disease across the continent has also resulted in novel genetic and phenotypic adaptations in extant Africans. This review summarizes some recent advances in our understanding of the demographic history and selective pressures that have influenced levels and patterns of diversity in African populations.